Of course, this is a little bit tongue-in-cheek. Like many other old-school pundits, I do think that Gygax's Dungeon Master's Guide is among the top books you should have and read in order to understand the classic game (and generally how to DM a D&D campaign). It's discursive, literary, free-wheeling, and gives great insight to the mindset of the creator. When I was a teenager, I would constantly bring the DMG with me on road trips and read its many lengthy passages on the game to try to understand them, and then re-read them again later on.
But it's not all wine-and-roses. Gygax made at least a few serious missteps in switching from Original D&D's little-brown-books to the AD&D hardcovers (or perhaps he took for granted certain knowledge from OD&D, and overlooked needing to reiterate those pieces in AD&D). He really could have used a strong 2nd-in-command editor figure, like an Arneson or a Holmes or someone like that. As a young player, I can recall many moments of semi-frustration trying to make certain parts of the game work; not until I acquired OD&D much later (start of this blog) did I see the origin of those components, and how much better they work in their original OD&D state.
The broad theme of these pieces will be: The perilous desire to take an early, satisfying game mechanic and make it over-generalized, too abstract, and non-concrete. Like: An attempt to "cover everyone's use cases" (thanks, XKCD!), or assuming that providing an abstract template and letting gamers "skin" it to their own game will be adequate (esp., thinking of the case of brand-new players). Stuff like that. Here's one short-ish early example: Disease.
Original D&D, Supplement II (Blackmoor): Diseases first appeared in Original D&D via Dave Arneson's Blackmoor supplement. Here's a bit of the introductory text and the key table (plus separate short paragraphs on each disease type and overall mechanics, running about 3 half-pages):
So: They key things here are that we're seeing real-world medieval diseases being given game mechanics -- the game refers to, and models, something outside itself; in addition to being playable, it's also a vehicle to learn more about our own world. The number of diseases is fairly limited; about a dozen, which is manageable and fairly memorable. And it's not a re-write of our core campaign sensibility; as the opening paragraph states, it's "optional, and primarily concerns the Gamemaster, as it is incumbent upon him to determine if the disease exists" (kind of like a new monster or trap type). You even get some explanation of designer attempt, about how diseases are important in our world, and thus the game. While I'm not totally thrilled with the mechanics as written, it's coherent enough that you get in and tweak them if you desire.
Advanced D&D, Dungeon Master's Guide: Now, here in the AD&D DMG you see what Gygax does to the system when he gets his hands on it:
Key point: In AD&D, you don't see specific diseases anymore; now they're fully abstracted and what you get is a severity, occurrence, and body area, in modern quasi-medical lingo, like a "mild, chronic nose-throat disorder" (quick, refer me to a good nose-throat specialist!). What you don't get is any in-world name for the disease (unless you want to make one up yourself or do outside research). Also, if you multiply out all the combinations of body part, occurrence, and severity, what you get is something like 110 different maladies; arguably a good thing if you want lots of variety, but too much for me (for example) to remember or name or get "system mastery" around as DM. And the introductory paragraphs don't make this sound like an option any more -- "Each game month check for each character to determine if he or she has become infested...". The section also appears very near the start of the DMG (page 13), even before ability scores, races, or classes are explained, making it seem even more like a core piece of the game campaign system.
As a young man, I indeed read this as a key expected component of the AD&D game, and I was regularly trying to roll that random 2% chance for disease & infestation on a weekly/monthly basis, as indicated. But more importantly, taking out concrete, named, player-identifiable and era-appropriate diseases and replacing them with abstract gobbledeygook is nigh-unforgivable to me.
3rd Edition D&D, Dungeon Master's Guide: Let's also check in on the much later 3rd Edition iteration:
Disease: When a character is injured by a contaminated attack, touches an item smeared with diseased matter, or consumes disease-tainted food or drink, he must make an immediate Fortitude saving throw. If he succeeds, the disease has no effect—his immune system fought off the infection. If he fails, he takes damage after an incubation period. Once per day afterward he must make a successful Fortitude saving throw to avoid repeated damage. Two successful saving throws in a row indicate that he has fought off the disease and recovers, taking no more damage.
Okay, so now we're back to a small number of specific diseases, and they once again have names. Only problem: In the evolution from OD&D to AD&D to 3E, they've lost any connection to the real world (or I'd even take myth or literature) and become pure fantasy, self-referential, gamist nonsense.
Summary: Looking at 3E, I honestly do think this material for diseases is better than the 1E AD&D system (and I was much relieved to see it when 3E was published). Concrete details beat abstract talking-at-me. But in my book, it's definitely beat out by Arneson's system in OD&D, which is even more anchored by being related to the real world. Say to a player that they've got "the plague" or "smallpox" and they immediately know what they're dealing with and how horrible it is -- they don't have to go parsing/interpreting game mechanics before getting a gut-feeling for the badness. And that's what role-playing should really be about; hitting you in the gut, immediately, with descriptive detail and then letting the mechanics support that drama with oracular dice rolls and similar means.
Recommended: Disease system in Original D&D Sup-II by Arneson. Use specific real-world diseases as a default basis if possible, and let the DM make up their own specific fantasy stuff for their own campaign if so inclined.